July 9th
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Yin et al. (2023) quantify newly generated proteins at a global level in several distinct types of human cells to examine protein inhibition. Rao et al. (2023) investigate the Eif4e1c family, members of which play roles in zebrafish heart development and regeneration. Lastly, Reynaud et al. (2023) carry out an unbiased analysis that measures regulatory activity across the budding yeast proteome.
Global quantification of newly synthesized proteins reveals cell type-and inhibitor-specific effects on protein synthesis inhibition
PNAS Nexus, 2023
Yin, K., Tong, M., Suttapitugsakul, S., Xu, S. and Wu, R.
Protein synthesis is frequently altered to gain further insight into how certain proteins function as well as cellular activity. The synthesis inhibition efficiency of individual proteins by various inhibitors at the proteome level are incredibly difficult to quantify and evaluate, despite the fact that many inhibitors have been extensively studied. Since newly generated proteins are the direct byproducts of protein synthesis, their quantification can aid in the study of protein inhibition. Here, the authors quantify newly generated proteins at a global level in several distinct types of human cells (A549, MCF-7, Jurkat, and THP-1 cells) to investigate protein inhibition and evaluate various common inhibitors, including cycloheximide, puromycin, and anisomycin.
By combining azidohomoalanine-based protein tagging, selective enrichment, a boosting strategy, and multiplexed proteomics, the inhibitory efficiencies of almost 5,000 newly synthesized proteins were determined. The synthesis inhibition efficiency for various proteins in the same cells vary dramatically when the same inhibitor is used, and each inhibitor also displays differences in efficiencies among different cell types. Moreover, in all cell types treated with each inhibitor, nucleolar and ribosomal proteins have relatively higher inhibitory efficiency, and proteins that are inherently sensitive to the inhibition or resistant to it are shown to have specific roles. Puromycin is the most non-discriminatory of these inhibitors, whereas cycloheximide is comparatively less effective at inhibiting the synthesis of ribosomal proteins.
The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration
Development, 2023
Rao, A., Lyu, B., Jahan, I., Lubertozzi, A., Zhou, G., Tedeschi, F., Jankowsky, E., Kang, J., Carstens, B., Poss, K.D., Baskin, K. and Goldman J.A.
The limiting step for mRNA translation is the binding of 5′ methylated caps by the eIF4E family of translation initiation factors. Although the canonical eIF4E1A is necessary for cell viability, there are several related eIF4E families that are used in specific contexts or tissues. Zebrafish regenerate heart muscle after severe injury, and in a prior study using ribosome profiling, this group discovered that the eif4e1c gene’s expression rises in zebrafish hearts during regeneration. Here, the authors describe the Eif4e1c family, members of which play roles in zebrafish heart development and regeneration. All aquatic vertebrates contain the Eif4e1c family, while all terrestrial species lack it. It is suggested that Eif4e1c works in a novel pathway because of an interface formed along the protein surface by a core group of amino acids shared over 500 million years of evolution.
CRISPR-generated zebrafish mutants with eif4e1c deletion experienced growth deficiencies and decreased juvenile survival. Adult mutants produced fewer cardiomyocytes and showed a diminished proliferative response to heart damage. Mutant hearts’ ribosome profiles revealed alterations in the mRNA translation efficiency of genes known to control cardiomyocyte proliferation. Despite the fact that eif4e1c is widely expressed, its disruption had the greatest effects on the heart and at the juvenile period.
Surveying the global landscape of post-transcriptional regulators
Nature Structural & Molecular Biology, 2023
Reynaud, K., McGeachy, A.M., Noble, D., Meacham, Z.A. and Ingolia, N.T.
Many proteins alter the translation and decay of mRNA to control gene expression. Here, the authors carry out an unbiased analysis that measures such regulatory activity across the budding yeast proteome and identifies the protein domains associated with these effects, in order to elucidate the entire range of the post-transcriptional regulators involved. Their method examines 50,000 protein fragments and determines their effects on a tethered mRNA using a tethered function assay and quantitative single-cell fluorescence measurements. With their approach, they were able to report hundreds of proteins, including highly active, non-canonical RNA binding proteins, that affect mRNA translation and stability.
In order to map the regulatory activity of proteins to specific domains and areas, proteins were divided into subsets. In some cases, this revealed effects that were not immediately clear in the context of the full-length protein. Protein domains and short peptide motifs were also found enriched among the most active post-transcriptional regulators thanks to this high level of resolution. Notably, despite the fact that many canonical RNAs binding proteins were active regulators, most of their regulatory activity did not map to the RNA binding domain. Their findings shed light on the molecular underpinnings of post-transcriptional gene regulation and identify networks of interacting proteins that regulate mRNA fate.
